EnzymeML – a data exchange format for biocatalysis and enzymology

EnzymeML is an XML–based data exchange format that supports the comprehensive documentation of enzymatic data by describing reaction conditions, time courses of substrate and product concentrations, the kinetic model, and the estimated kinetic constants. EnzymeML is based on the Systems Biology Markup Language, which was extended by implementing the STRENDA Guidelines. An EnzymeML document serves as a container to transfer data between experimental platforms, modelling tools, and databases. EnzymeML supports the scientific community by introducing a standardised data exchange format to make enzymatic data findable, accessible, interoperable, and reusable according to the FAIR data principles. An Application Programming Interface in Python and Java supports the integration of applications. The feasibility of a seamless data flow using EnzymeML is demonstrated by creating an EnzymeML document from a structured spreadsheet or from a STRENDA DB database entry, by kinetic modelling using the modelling platform COPASI, and by uploading to the enzymatic reaction kinetics database SABIO-RK.

Camtrap DP: A frictionless data exchange format for camera trapping data

Camera trapping is one of the most important technologies in conservation and ecological research and a well-established, non-invasive method of collecting field data on animal abundance, distribution, behaviour, temporal activity, and space use (Wearn and Glover-Kapfer 2019). Collectively, camera trapping projects are generating a massive and continuous flow of data, consisting of images and videos (with and without animal observations) and associated identifications (Scotson et al. 2017, Kays et al. 2020). In recent years, significant progress has been made by the global camera trapping community to resolve the challenges this brings, from the development of specialized data management tools and analytical packages, to the application of cloud computing and artificial intelligence to automate species recognition (Tabak et al. 2018). However, to effectively exchange camera trap data between infrastructures and to (automatically) harmonize data into large-scale wildlife datasets, there is a need for a common data exchange format—one that captures the essential information about a camera trap study, allows expression of different study and identification approaches, and aligns well with existing biodiversity standards such as Darwin Core (Wieczorek et al. 2012). Here we present Camera Trap Data Package (Camtrap DP), a data exchange format for camera trap data. It is managed by the Machine Observations Interest Group of Biodiversity Information Standards (TDWG) and developed publicly, soliciting community feedback for every change. Camtrap DP is built on Frictionless Standards, a set of generic specifications to describe and package (tabular) data and metadata. Camtrap DP extends these with specific requirements and constraints for camera trap data. By building on an existing framework, users can employ existing open source software to read and validate Camtrap DP formatted data. Validation especially is useful to automatically check if provided data meets the requirements set forth by Camtrap DP, before analysis or integration. Supported by the major camera trap data management systems e.g. Agouti, TRAPPER, eMammal, and Wildlife Insights, Camtrap DP is reaching its first stable version. The first Camtrap DP dataset was published on Zenodo (Cartuyvels et al. 2021b). This dataset was also published to the Global Biodiversity Information Facility (GBIF) (Cartuyvels et al. 2021a), demonstrating the ability and limitations of transforming the data to the Darwin Core standard.

SPART, a versatile and standardized data exchange format for species partition information

A wide range of data types can be used to delimit species and various computer-based tools dedicated to this task are now available. Although these formalized approaches have significantly contributed to increase the objectivity of SD under different assumptions, they are not routinely used by alpha-taxonomists. One obvious shortcoming is the lack of interoperability among the various independently developed SD programs. Given the frequent incongruences between species partitions inferred by different SD approaches, researchers applying these methods often seek to compare these alternative species partitions to evaluate the robustness of the species boundaries. This procedure is excessively time consuming at present, and the lack of a standard format for species partitions is a major obstacle. Here we propose a standardized format, SPART, to enable compatibility between different SD tools exporting or importing partitions. This format reports the partitions and describes, for each of them, the assignment of individuals to the inferred species. The syntax also allows to optionally report support values, as well as original trees and the full command lines used in the respective SD analyses. Two variants of this format are proposed, overall using the same terminology but presenting the data either optimized for human readability (matricial SPART) or in a format in which each partition forms a separate block (SPART.XML). ABGD, DELINEATE, GMYC, PTP and TR2 have already been adapted to output SPART files and a new version of LIMES has been developed to import, export, merge and split them.

Qiime Artifact eXtractor (qax): A Fast and Versatile Tool to Interact with Qiime2 Archives

Qiime2 is one of the most popular software tools used for analysis of output from metabarcoding experiments (e.g., sequencing of 16S, 18S, or ITS amplicons). Qiime2 introduced a novel and innovative data exchange format: the ‘Qiime2 artifact’. Qiime2 artifacts are structured compressed archives containing a dataset and its associated metadata. Examples of datasets are FASTQ reads, representative sequences in FASTA format, a phylogenetic tree in Newick format, while examples of metadata are the command that generated the artifact, information on the execution environment, citations on the used software, and all the metadata of the artifacts used to produce it. While artifacts can improve the shareability and reproducibility of Qiime2 workflows, they are less easily integrated with general bioinformatics pipelines. Accessing metadata in the artifacts also requires full Qiime2 installation. Qiime Artifact eXtractor (qax) allows users to easily interface with Qiime2 artifacts from the command line, without needing the full Qiime2 environment installed (or activated).

Recent Trends in JSON Filters

JavaScript Object Notation is a text-based data exchange format for structuring data between a server and web application on the client-side. It is basically a data format, so it is not limited to Ajax-style web applications and can be used with API’s to exchange or store information. However, the whole data never to be used by the system or application, It needs some extract of a piece of requirement that may vary person to person and with the changing of time. The searching and filtration from the JSON string are very typical so most of the studies give only basics operation to query the data from the JSON object. The aim of this paper to find out all the methods with different technology to search and filter with JSON data. It explains the extensive results of previous research on the JSONiq Flwor expression and compares it with the json-query module of npm to extract information from JSON. This research has the intention of achieving the data from JSON with some advanced operators with the help of a prototype in json-query package of NodeJS. Thus, the data can be filtered out more efficiently and accurately without the need for any other programming language dependency. The main objective is to filter the JSON data the same as the SQL language query.